As you suggested, I made a separate extension. It just contains copies of "Allied Unit" and "Axis Unit" prototypes from the base module, to which I added traits for formation color and inactivity. When saving the extension, the editor warns that there are two definitions of prototypes, but some testing did not show any problems.
Originally I did not think it would work and I would have to edit the traits in the base module, as
Vassal 3.1 Designer's Guide p. 106 states
Quote:What an Extension Canʼt Do
...
- Modify, replace, or override Prototype Definitions from the base module.
but I am not complaining. If we run into problems, we can disable the extension and improvise an another way.